Multiple platform build/check report for BioC 3.6 - CHECK report for readat on tokay1

Package: readat

Version: 1.4.0

Command: rm -rf readat.buildbin-libdir readat.Rcheck && mkdir readat.buildbin-libdir readat.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=readat.buildbin-libdir readat_1.4.0.tar.gz >readat.Rcheck\00install.out 2>&1 && cp readat.Rcheck\00install.out readat-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=readat.buildbin-libdir --install="check:readat-install.out" --force-multiarch --no-vignettes --timings readat_1.4.0.tar.gz

StartedAt: 2018-04-12 02:33:34 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:37:35 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 240.8 seconds

RetCode: 0

Status: WARNINGS

CheckDir: readat.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf readat.buildbin-libdir readat.Rcheck && mkdir readat.buildbin-libdir readat.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=readat.buildbin-libdir readat_1.4.0.tar.gz >readat.Rcheck\00install.out 2>&1 && cp readat.Rcheck\00install.out readat-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=readat.buildbin-libdir --install="check:readat-install.out" --force-multiarch --no-vignettes --timings readat_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/readat.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'readat/DESCRIPTION' ... OK
* this is package 'readat' version '1.4.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'readat' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpA1NbA9/R.INSTALL370440ae1aec/readat/man/chromosomalPositions.Rd:7: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpA1NbA9/R.INSTALL370440ae1aec/readat/man/chromosomalPositions.Rd:8: missing file link 'GRanges'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/readat.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
sfread: no visible binding for global variable 'header'
sfread: no visible binding for global variable 'nrows'
Undefined global functions or variables:
  header nrows
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/readat.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'readat' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'readat'
    finding HTML links ... done
    WideSomaLogicData                       html  
    WideSomaLogicDataAttributes             html  
    aptamers                                html  
    as.ExpressionSet                        html  
    as.SummarizedExperiment                 html  
    chromosomalPositions                    html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpA1NbA9/R.INSTALL370440ae1aec/readat/man/chromosomalPositions.Rd:7: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpA1NbA9/R.INSTALL370440ae1aec/readat/man/chromosomalPositions.Rd:8: missing file link 'GRanges'
    colnamesStartWithSeqId                  html  
    convertSeqIdToAptamer                   html  
    createSampleSubmission                  html  
    ensemblIds                              html  
    extractSampleData                       html  
    getChromosomalPositions                 html  
    getEnsemblIds                           html  
    getGoMolecularFunctions                 html  
    getKeggDefinitions                      html  
    getPfam                                 html  
    getSampleIdVar                          html  
    getSequencesWithLargestBetweenGroupVariation
                                            html  
    getUniProtKeywords                      html  
    goMolecularFunction                     html  
    isPass                                  html  
    isSomaEset                              html  
    keggDefinitions                         html  
    melt.WideSomaLogicData                  html  
    orderPlatePosition                      html  
    pfam                                    html  
    readAdat                                html  
    readComments                            html  
    readControls                            html  
    readFirstChar                           html  
    readSamples                             html  
    readSlides                              html  
    readat-defunct                          html  
    sub-.WideSomaLogicData                  html  
    uniprotKeywords                         html  
    writeSampleSubmissionForm               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'readat' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'readat' as readat_1.4.0.zip
* DONE (readat)
In R CMD INSTALL
In R CMD INSTALL


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(readat)
> library(testthat)
> 
> test_check("readat")
== testthat results  ===========================================================
OK: 62 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   6.25    0.26    7.00


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(readat)
> library(testthat)
> 
> test_check("readat")
== testthat results  ===========================================================
OK: 62 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   7.59    0.15    7.84

name	user	system	elapsed
WideSomaLogicData	0.00	0.02	0.01
WideSomaLogicDataAttributes	1.32	0.02	1.39
aptamers	0.00	0.01	0.02
as.ExpressionSet	2.26	0.14	2.64
as.SummarizedExperiment	0.40	0.00	0.46
chromosomalPositions	0.43	0.00	0.43
colnamesStartWithSeqId	0.23	0.03	0.32
convertSeqIdToAptamer	0	0	0
ensemblIds	0	0	0
extractSampleData	0.02	0.00	0.04
getChromosomalPositions	0.09	0.00	0.09
getEnsemblIds	0	0	0
getGoMolecularFunctions	0.19	0.00	0.19
getKeggDefinitions	0.03	0.00	0.03
getPfam	0.01	0.00	0.01
getUniProtKeywords	0.02	0.00	0.02
goMolecularFunction	0.45	0.02	0.47
keggDefinitions	0.03	0.00	0.03
pfam	0.02	0.00	0.02
readAdat	0.33	0.00	0.39
readComments	0.03	0.00	0.03
readControls	0.36	0.00	0.36
readSamples	0.12	0.00	0.13
readSlides	0.14	0.00	0.14
sub-.WideSomaLogicData	0.29	0.02	0.36
uniprotKeywords	0.01	0.00	0.01
writeSampleSubmissionForm	0.11	0.03	0.28

name	user	system	elapsed
WideSomaLogicData	0.02	0.00	0.02
WideSomaLogicDataAttributes	1.14	0.00	1.20
aptamers	0	0	0
as.ExpressionSet	3.16	0.15	3.56
as.SummarizedExperiment	0.45	0.00	0.59
chromosomalPositions	0.17	0.00	0.17
colnamesStartWithSeqId	0.35	0.00	0.41
convertSeqIdToAptamer	0	0	0
ensemblIds	0	0	0
extractSampleData	0.01	0.00	0.02
getChromosomalPositions	0.11	0.00	0.11
getEnsemblIds	0.02	0.00	0.01
getGoMolecularFunctions	0.62	0.00	0.63
getKeggDefinitions	0.02	0.00	0.01
getPfam	0	0	0
getUniProtKeywords	0.02	0.00	0.01
goMolecularFunction	0.56	0.00	0.57
keggDefinitions	0.03	0.00	0.03
pfam	0.02	0.00	0.01
readAdat	0.42	0.02	0.72
readComments	0.02	0.00	0.02
readControls	0.43	0.00	0.43
readSamples	0.16	0.00	0.16
readSlides	0.17	0.00	0.17
sub-.WideSomaLogicData	0.47	0.01	0.55
uniprotKeywords	0.03	0.00	0.03
writeSampleSubmissionForm	0.21	0.00	0.28

CHECK report for readat on tokay1

Summary

Command output

Installation output

Tests output

Example timings